New ”tree of life” constructed for one of the largest groups of bacteria

Researchers at the Virginia Bioinformatics Institute (VBI) at Virginia Tech have created a new “tree of life” for the gamma-proteobacteria— a large group of medically and scientifically important bacteria that includes Escherichia coli, Salmonella typhimurium, and other disease-causing organisms.

By building powerful phylogenetic trees, scientists can quickly identify similarities and differences between the make-up of many different organisms.

They also provide crucial information in the search for treatments to fight anything from the bugs that cause food poisoning to the pathogens that cause life-threatening diseases such as cholera and the plague.

A “tree of life,” or phylogenetic tree, is a way to visualize the evolutionary relationships among different biological species that have descended from a common ancestor.

The gamma-proteobacteria tree developed by VBI researchers was reconstructed using powerful computers from as many as 30 million data points of bacterial sequence information.

“Ribosomal RNA is one of the central components of the ribosome, the protein manufacturing machinery of all living cells. In the past, researchers have often depended on looking at a single ribosomal RNA gene to construct evolutionary relationships for their tree-building efforts. The method we use to make our tree of life uses hundreds of different genes and integrates much more information than can be gleaned from the traditional single gene approach. We firmly believe that the multi-gene or phylogenomics approach should become the standard for tree building when several genome sequences are available, which is now the case for most bacterial groups,” said Kelly Williams, Research Investigator at VBI.

The researchers selected 108 available genomes from the more than 200 complete and partial sequences available for the gamma-proteobacteria, placing the emphasis on the diversity of the bacterial species and quality of the original sequence data.

“The consensus tree that we have put together for the gamma-proteobacteria is a powerful tool that can be used to predict shared biology and analyze, for example, the novel ways that bacteria have adapted to their living environments. Phylogenomics provides for very accurate reconstructions of inheritance from common ancestors,” said Allan Dickerman, Assistant Professor at VBI.

The researchers looked at a very large class of bacteria that lack a well-resolved phylogenetic tree.

By placing emphasis on searches for single-copy genes, the scientists could radically improve the resolution of the evolutionary tree.

“Some parts of our tree were still not fully resolved, but we believe that future work will improve our method further to handle these deficiencies,” said Williams.